Control cable length is not the issue. That will probably be fine. The motor ends of the control cables are different, though.
Mercury and Johnnyrude shifters are different. Mercury pushes the throttle closed. Johnnyrude pulls the throttle closed.
A lot of aftermarket (non Merc or Johnnyrude) controls can be converted to work for either motor. They need to be disassembled and the internal pivot points changed. You may be able to find instructions to do this on the OEM web site.